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# Description of the functions concerning the element definition

## Description of the functions of the API

 defineCovariateElement Define a new covariate element. defineIndividualElement Define a new individual element. defineOccasionElement Define a new occasion element. defineOutputElement Define a new output element. definePopulationElement Define a new population element. defineRegressorElement Define a new regression element. defineTreatmentElement Define a new treatmen element. deleteElement Delete an element of any type. getCovariateElements Get the list of all available covariate elements for the exploration and simulation. getIndividualElements Get the list of all available individual elements for the exploration and simulation. getOccasionElements Get the list of the occasion element for the simulation. getOutputElements Get the list of all available output elements for the exploration and simulation. getPopulationElements Get the list of all available population elements for the simulation. getRegressorElements Get the list of all available regressor elements for the exploration and simulation. getTreatmentElements Get the list of all available treatments elements for the exploration and simulation.

## [Simulx] Define covariate element

### Description

Define a new covariate element. If can be defined as an external file or as a data.frame. If defined by a data.frame, it can contain only one row. #’ @examples

### Usage

defineCovariateElement(name, element)


 getCovariateElements

## Not run:

defineCovariateElement(name = “name”, element = “file/path”)

defineCovariateElement(name = “name”, element = data.frame(WEIGHT = 70.5, SEX = “M”))

## End(Not run)

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## [Simulx] Define individual element

### Description

Define a new individual element. If can be defined an external file or as a data.frame.#’ @examples
## Not run:
defineIndividualElement(name = “name”, element = “file/path”)
defineIndividualElement(name = “name”, element = data.frame(Cl = 1, V = 2.5))
defineIndividualElement(name = “name”, element = data.frame(Cl = c(1, 2), V = c(2.5, 5)
## End(Not run)

### Usage

defineIndividualElement(name, element)


 getIndividualElements

## [Simulx] Define occasion element

### Description

Define a new occasion element. If can be defined an external file or as a data.frame. Only one occasion element can be defined.

### Usage

defineOccasionElement(element)


 getOccasionElements

## Not run:

defineOccasionElement(element = “file/path”)

defineOccasionElement(element = data.frame(time = c(0, 0.5, 2), occ1 = c(1, 1, 2), occ2 = c(1, 2, 3)))

## End(Not run)

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## [Simulx] Define output element

### Description

Define a new output element. If can be defined an external file or as a data.frame.

### Usage

defineOutputElement(name, element)


 getOutputElements

## Not run:

defineOutputElement(name = “name”, element = list(data = “file/path”, output = “output”))

defineOutputElement(name = “name”, element = list(data = data.frame(time = c(1.25, 2, 5.5)), output = “output”))

defineOutputElement(name = “name”, element = list(data = data.frame(time = c(0, 2, 3, 4, 5), occ1 = c(1, 1, 1, 2, 2), occ2 = c(1, 1, 2, 1, 2)), output = “output”))

defineOutputElement(name = “name”, element = list(data = data.frame(start = 1, interval = 10, final = 100), output = “output”))

defineOutputElement(name = “name”, element = list(data = data.frame(start = c(1, 1, 1, 1), interval = c(10, 5, 10, 5), final = c(100, 120, 150, 200)), output = “output”))

## End(Not run)

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## [Simulx] Define population element

### Description

Define a new population element. If can be defined an external file or as a data.frame.

### Usage

definePopulationElement(name, element)


 getPopulationElements

## Not run:

definePopulationElement(name = “name”, element = “file/path”)

definePopulationElement(name = “name”, element = data.frame(Cl_pop = 1, V_pop = 2.5))

definePopulationElement(name = “name”, element = data.frame(Cl_pop = c(1, 3), V_pop = c(2.5, 6))

## End(Not run)

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## [Simulx] Define regressor element

### Description

Define a new regression element. If can be defined an external file or as a data.frame.

### Usage

defineRegressorElement(name, element)


 getRegressorElements

## Not run:

defineRegressorElement(name = “name”, element = “file/path”)

defineRegressorElement(name = “name”, element = data.frame(time = c(0, 0.5, 2), reg1 = c(1, 2, 5.25), reg2 = c(0, 0.25, 1)))

defineRegressorElement(name = “name”, element = data.frame(time = c(0, 0.5, 2, 5, 6), reg1 = c(1, 2, 5.25, 6, 7), reg2 = c(0, 0.25, 1, 2, 3), occ1 = c(1,1,1,2,2), occ2 = c(1,1,2,1,2)))

## End(Not run)

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## [Simulx] Define treatment element

### Description

Define a new treatment element. If can be defined an external file or as a data.frame.

### Usage

defineTreatmentElement(name, element)


### Note

admID, repeat and probaMissDose are optional. In data, tInf and reset are optional.

 getTreatmentElements

## Not run:

defineTreatmentElement(name = “name”, element = list(data = “file/path”))

defineTreatmentElement(name = “name”, element = list(probaMissDose=0, admID=1, repeats=c(cycleDuration = 1, NumberOfRepetitions=12), data=data.frame(time=c(1,2), amount=c(1,2), tInf=c(0, 1), reset=c(TRUE, FALSE))))

defineTreatmentElement(name = “name”, element = list(probaMissDose=0, admID=1, repeats=c(cycleDuration = 1, NumberOfRepetitions=12), data=data.frame(time=c(10,10,10,10), amount=c(10,20,30,40), occ1=c(1,1,2,2), occ2=c(1,2,1,2))))

defineTreatmentElement(name = “name”, element = list(probaMissDose=0, admID=1, repeats=c(cycleDuration = 1, NumberOfRepetitions=12), data=data.frame(start=1, interval=2, nbDoses=10, amount=1)))

## End(Not run)

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## [Simulx] Delete element

### Description

Delete an element of any type.

### Usage

deleteElement(name)


## Not run:

deleteElement(name = “name”)

## End(Not run)

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## [Simulx] Get covariate elements

### Description

Get the list of all available covariate elements for the exploration and simulation.
Each element is a list of

 “inputType” (string) Type of input definition: can be “manual”, “distribution” or “external”. “file” (string) Path to the file if the inputType is external. NULL else wise. “data” (data.frame) Values of the element.

Notice that:
– if the project was created from a model file, an covariate element Covariates is created with all values equal 1.
– if the project was created using a Monolix project,
– an covariate element mlx_Cov is created with the values corresponding of the covariates values of the project.
– an covariate element mlx_CovDist is created with the values corresponding of the esimation of the distribution of the covariates of the project.

### Usage

getCovariateElements(name)


 defineCovariateElement

## Not run:

getCovariateElements()

$mlx_Cov #’$mlx_Cov$inputType [1] “external”$mlx_Cov$file [1] path/to/file$mlx_Cov$data id WEIGHT 1 1 79.6 2 2 72.4 3 3 70.5 4 4 72.7 5 5 54.6$covMan

$covMan$inputType

[1] “manual”

$covMan$file

NULL

$covMan$data

id WEIGHT

1 common 75

## End(Not run)

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## [Simulx] Get individual elements

### Description

Get the list of all available individual elements for the exploration and simulation.
Each element is a list of

 “inputType” (string) Type of input definition: can be “manual” or “external”. “file” (string) Path to the file if the inputType is external. NULL else wise. “data” (data.frame) Values of the element.

Notice that:
– if the project was created from a model file, an individual element IndivParameters is created with all values equal 1.
– if the project was created using a Monolix project,
– an individual element mlx_IndivInit is created with the values corresponding of the initial population parameters if the population parameters were not estimated.
– an individual element mlx_PopIndiv is created with the values corresponding of the estimated population parameters (without the covariate(s) impact(s)) if the population parameters were estimated.
– an individual element mlx_PopIndivCov is created with the values corresponding of the estimated population parameters (with the covariate(s) impact(s)) if the population parameters were estimated.
– an individual element mlx_EBEs is created with the values corresponding of the estimated EBEs if the EBEs were estimated.
– an individual element mlx_CondMean is created with the values corresponding of the estimated conditional mean if the conditional distribution task was perfored.
– an individual element mlx_CondDistSample is created with the values corresponding of the first sample of the conditional ditribution if the conditional distribution task was perfored.

### Usage

getIndividualElements()


 defineIndividualElement

## Not run:

getIndividualElements()

$mlx_PopIndiv$mlx_PopIndiv$inputType [1] “manual”$mlx_PopIndiv$file NULL$mlx_PopIndiv$data id Cl V1 Q2 V2 Q3 V3 1 common 2.462069 4.557752 0.1151846 4.355022 1.70242 8.229753$mlx_EBEs

$mlx_EBEs$inputType

[1] “external”

$mlx_EBEs$file

[1] file/to/path

$mlx_EBEs$data

id Cl V1 Q2 V2 Q3 V3

1 1 2.870556 5.801418 2.12758339 5.963084 0.6649303 13.069996

2 2 2.899189 4.443222 0.31646327 5.226719 2.3678264 9.182623

## End(Not run)

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## [Simulx] Get occasion elements

### Description

Get the list of the occasion element for the simulation. It is a list of

 “id” (string) Ids of the occastions “names” (string) Name of the occasions. “times” (data.frame) Times of the occasions. “occasions” (data.frame) Values of the element.

### Usage

getOccasionElements()


 defineOccasionElement

## [Simulx] Get output elements

### Description

Get the list of all available output elements for the exploration and simulation.
Each element is a list of

 “output” (string) Output name. “inputType” (string) Type of input definition: can be “manual” or “external”. “file” (string) Path to the file if the inputType is external. NULL else wise. “data” (data.frame) Values of the element.

Importantly, all the variables in the model file can be used as an output. The user is not consrtrained to the ones defined in the OUTPUT: section.
Notice that:
– if the project was created from a model file, an outpout element is created for each output of the section OUTPUT: with regular grid from 0 to 100 by 1.
– if the project was created using a Monolix project, with for exemple CC as a predicition and y as measurement
– an individual element mlx_y1 is created as an external file with the values corresponding of the output values for each id of the project.
– an individual element mlx_Cc is created with a regular grid starting from the first time measurement of the project to the final time measurement of the project.

### Usage

getOutputElements()


 defineOutputElement

## Not run:

$output [1] “y1”$inputType

[1] “manual”

$file NULL$data

id time

1 common 0

2 common 1

3 common 2

## End(Not run)

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## [Simulx] Get population elements

### Description

Get the list of all available population elements for the simulation.
Each element is a list of

 “inputType” (string) Type of input definition: can be “manual” or “external”. “file” (string) Path to the file if the inputType is external. NULL else wise. “data” (data.frame) Values of the element.

Notice that:
– if the project was created from a model file, a population element PopParameters is created with all values equal 1.
– if the project was created using a Monolix project,
– a population element mlx_Pop is created with the values corresponding of the Monolix estimated population parameters.
– a population element mlx_PopInit is created with the values corresponding of the Monolix initial population parameters if the parameters were not estimated.

### Usage

getPopulationElements()


 definePopulationElement

## Not run:

getPopulationElements()

$mlx_Pop$mlx_Pop$inputType [1] “manual”$mlx_Pop$file NULL$mlx_Pop$data id Cl_pop V1_pop Q2_pop V2_pop Q3_pop V3_pop omega_Cl omega_Q2 omega_Q3 omega_V1 omega_V2 omega_V3 b 1 common 2.462069 4.557752 0.1151846 4.355022 1.70242 8.229753 0.2272315 0.92641 0.5745623 0.4080015 0.8127517 0.4464604 0.1106325 ## End(Not run) Top of the page, PKanalix R-functions, Monolix R-functions, Simulx R-functions. ## [Simulx] Get regressor elements ### Description Get the list of all available regressor elements for the exploration and simulation. Each element is a list of  “inputType” (string) Type of input definition: can be “manual” or “external”. “file” (string) Path to the file if the inputType is external. NULL else wise. “data” (data.frame) Values of the element. ### Usage getRegressorElements()  ### See Also  defineRegressorElement ### Click here to see examples ## Not run:$inputType

[1] “manual”

$file NULL$data

id time

1 common 0

2 common 1

3 common 2

## End(Not run)

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## [Simulx] Get treatment elements

### Description

Get the list of all available treatments elements for the exploration and simulation.
Each element is a list of

 “inputType” (string) Type of input definition: can be “manual” or “external”. “file” (string) Path to the file if the inputType is external. NULL else wise. “data” (data.frame) Values of the element.

Notice that:
– if the project was created from a model file, no treatment is added.
– if the project was created using a Monolix project, for each administraion type of the project,
– an individual element mlx_adm is created as an external file with the values corresponding of the treatment values for each id of the project.

### Usage

getTreatmentElements()


 defineTreatmentElement

## Not run:

$mlx_Adm1$mlx_Adm1$inputType [1] “external”$mlx_Adm1$file [1] path/to/file$mlx_Adm1\$data

id time amount washout

1 1 0 320 FALSE

2 2 0 320 FALS

## End(Not run)

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